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PubMed2000

High-efficiency transient transfection of endothelial cells for functional analysis.

The definition of signaling pathways in endothelial cells has been hampered by the difficulty of transiently transfecting these cells with high efficiency. This investigation was undertaken to develop an efficient technique for the transfection of endothelial cells for functional analyses. Cells cotransfected with plasmid expressing green fluorescent protein (GFP) and the plasmid of interest were isolated by fluorescence-activated cell sorting (FACS) based on GFP expression. In the sorted cell population, a 2.5-fold enhancement in the number of cells expressing the gene of interest was observed, as confirmed by FACS analysis and Western blotting. Sorted cells retained functional properties, as demonstrated by chemotaxis to the agonist sphingosine 1-phosphate (SPP). To demonstrate the usefulness of this method for defining cellular signaling pathways, cells were cotransfected with plasmids encoding GFP and the carboxyl-terminal domain of the beta-adrenergic receptor kinase (beta ARKct), which inhibits signaling through the beta gamma dimer of heterotrimeric G-proteins. SPP-induced chemotaxis in sorted cells coexpressing beta ARKct was inhibited by 80%, demonstrating that chemotaxis was driven by a beta gamma-dependent pathway. However, no significant inhibition was observed in cells transfected with betaARKct but not enriched by sorting. Thus, we have developed a method for enriching transfected cells that allows the elucidation of crucial mechanisms of endothelial cell activation and function. This method should find wide applicability in studies designed to define pathways responsible for regulation of motility and other functions in these dynamic cells.

Animals↗
PubMed1994

Complications in the functional analysis of transfected MHC genes.

Analysis of the relationship between the structure of a protein molecule and its function often exploits the techniques of gene mutation and expression in transfected cell lines. This approach has been used extensively in the study of MHC molecules for testing predictions derived from structural models. Comparison of the functional properties of mutant molecules is difficult because MHC molecules interact with both peptides and T cell receptors. Functionality is commonly determined in biological assays which are dependent on T cell recognition of specific peptide/MHC complexes and measure secondary events triggered by T cell activation. In this study four L cell lines transfected with different combinations of alpha and beta chains from I-Ak and I-Au were used as antigen-presenting cells to activate two hen egg-white lysozyme-specific T cell clones. We compared several biological assays, namely, T cell proliferation, cytokine production, and cytotoxicity. Different assays indicated varying degrees of functionality for the same MHC molecule and thus demonstrated the difficulty in unambiguous interpretation of data from complex assays. Furthermore, we detected differences among the transfected lines which appeared unrelated to the expression of the introduced MHC genes.

Animals↗
PubMed1999

Structure-function analysis of tritrypticin, an antibacterial peptide of innate immune origin.

The structural requirements for the antibacterial activity of a pseudosymmetric 13-residue peptide, tritrypticin, were analyzed by combining pattern recognition in protein structures, the structure-activity knowledge-base, and circular dichroism. The structure-activity analysis, based on various deletion analogs, led to the identification of two minimal functional peptides, which by themselves exhibit adequate antibacterial activity against Escherichia coli and Salmonella typhimurium. The common features between these two peptides are that they both share an aromatic-proline-aromatic (ArProAr) sequence motif, and their sequences are retro with respect to one another. The pattern searches in protein structure data base using the ArProAr motif led to the identification of two distinct conformational clusters, namely polyproline type II and beta-turn, which correspond to the observed solution structures of the two minimal functional analogs. The role of different residues in structure and function of tritrypticin was delineated by analyzing antibacterial activity and circular dichroism spectra of various designed analogs. Three main results arise from this study. First, the ArProAr sequence motif in proteins has definitive conformational features associated with it. Second, the two minimal bioactive domains of tritrypticin have entirely different structures while having equivalent activities. Third, tritrypticin has a beta-turn conformation in solution, but the functionally relevant conformation of this gene-encoded peptide antibiotic may be an extended polyproline type II.

Amino Acid Sequence↗
PubMed1990

Functional analysis of a centromere from fission yeast: a role for centromere-specific repeated DNA sequences.

A circular minichromosome carrying functional centromere sequences (cen2) from Schizosaccharomyces pombe chromosome II behaves as a stable, independent genetic linkage group in S. pombe. The cen2 region was found to be organized into four large tandemly repeated sequence units which span over 80 kilobase pairs (kb) of untranscribed DNA. Two of these units occurred in a 31-kb inverted repeat that flanked a 7-kb central core of nonhomology. The inverted repeat region had centromere function, but neither the central core alone nor one arm of the inverted repeat was functional. Deletion of a portion of the repeated sequences that flank the central core had no effect on mitotic segregation functions or on meiotic segregation of a minichromosome to two of the four haploid progeny, but drastically impaired centromere-mediated maintenance of sister chromatid attachment in meiosis I. This requirement for centromere-specific repeated sequences could not be satisfied by introduction of random DNA sequences. These observations suggest a function for the heterochromatic repeated DNA sequences found in the centromere regions of higher eucaryotes.

Base Sequence↗
PubMed2006

Functional analysis of the nuclear proteome of human A549 alveolar epithelial cells by HPLC-high resolution 2-D gel electrophoresis.

The airway epithelial cell plays a central role in coordinating airway inflammatory responses, where significant changes in the proteome occur in response to infectious stimuli. To further understand the spectrum of proteins and the biological processes they control, we have initially determined the nuclear proteome of human type II-like alveolar epithelial cells (A549) using a sequential method of organellar enrichment followed by HPLC prefractionation prior to 2-DE-based protein identification using MALDI-TOF MS. This approach yielded 719 high-confidence identifications, 433 mapping to unique gene identifiers. Expert classification showed that these proteins controlled chromatin remodeling, protein refolding, cytoskeletal structure, membrane function, metabolic processes, mitochondrial function, RNA binding, protein synthesis, signaling, and transcription factor activities. The proteins were mapped to gene ontology classifications, where metabolism and catalytic activity functions were significantly enriched, representing 43 and 32% of the protein set, respectively. Pathways analysis indicated a protein network affecting tumor necrosis factor-nuclear factor-kappaB signaling pathway interacting with intermediate cytoskeletal filaments. Forty-five proteins of unknown function were subjected to domain analysis and inferred to have additional nuclear functions controlling purine nucleotide metabolism and protein-protein interactions. This database represents the most comprehensive data set of mammalian nuclear proteins and will serve as a foundation for further discovery.

Cell Line, Transformed↗
PubMed1996

P2U purinoceptors: cDNA cloning, signal transduction mechanisms and structure-function analysis.

The cloning of a P2U purinoceptor cDNA has made it possible to use molecular biological approaches to investigate P2U purinoceptor function. Expression of recombinant P2U purinoceptors in mammalian cells lacking endogenous P2U purinoceptors has enabled us to characterize the receptor protein and its downstream effectors, and has allowed a partial analysis of the role of certain amino acid residues in ligand binding. These approaches have placed the pharmacological classification of the P2U purinoceptor on a firm molecular footing and have generated model systems that can be used to investigate receptor-ligand binding, regulation and signal transduction.

Amino Acid Sequence↗
PubMed2003

Functional analysis of the EGF-like domain mutations Pro55Ser and Pro55Leu, which cause mild hemophilia B.

We studied the functional role of two mutations, Pro55Ser and Pro55Leu, located in the N-terminal Epidermal Growth Factor-like domain (EGF1) of coagulation factor (F) IX. Both mutations cause mild hemophilia B with habitual FIX coagulant activities of 10-12% and FIX antigen levels of 50%. We found that activation by FVIIa/TF and FXIa was normal for FIXPro55Ser, but resulted in proteolysis of FIXPro55Leu at Arg318-Ser319 with a concomitant loss of amidolytic activity, suggesting intramolecular communication between EGF1 and the serine protease domain in FIX. This was further supported by experiments using an anti-EGF1 monoclonal antibody. Activation of FX by FIXaPro55Ser was impaired in both the presence and the absence of phospholipid or FVIIIa, indicating that Pro55 is not directly involved in binding to FVIIIa. We also studied the effect of the two Pro55 mutations on Ca2+ affinity and found only small changes. Thus, the Pro55Ser mutation causes hemophilia primarily through to an impaired ability to activate FX whereas at least in vitro the Pro55Leu defect interferes with the activation of FIX.

Calcium↗
PubMed2002

A virtual reality-based system for hand function analysis.

The goal of this study was to demonstrate the usability and usefulness of virtual reality technology in assessing hand functions. Ten healthy, non-disabled right-handed adult volunteers were recruited. Each volunteer used a dataglove to insert three-dimensional virtual representations of a cylinder and a prism into the target holes. To verify the reliability of the tests, each subject was retested twice. The performance testing assessed the visual-motor coordination a person needs to achieve a task accurately and within a set time. For each trial, the root mean square (RMS) value of the hand movement trajectory was projected onto the X, Y, and Z axes. This projection enabled us to measure the extent of the genuine, summative displacement of the manipulating hand. The reproducibility of the virtual reality assessment was analyzed using the intraclass correlation (ICC) approach. The total ICC values of 10 subjects demonstrated a high task completion time and RMS on the X and Z axes for the transferring of the prism. However, the values were low for the transferring of the cylinder. Because the individual coefficients of variations (CVs) varied widely in the moving of both the cylinder and the prism, the total (CVs) showed a high reading for the task completion time. Although rehabilitation clinics routinely carry out peg-moving exercises for disabled patients, our model provides a valuable quantitative real time and off-line measure of whole hand functions.

Adult↗
PubMed2003

Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis.

Mycobacterium tuberculosis, a Gram-positive bacterium, encodes a secreted Dsb-like protein annotated as Mtb DsbE (Rv2878c, also known as MPT53). Because Dsb proteins in Escherichia coli and other bacteria seem to catalyze proper folding during protein secretion and because folding of secreted proteins is thought to be coupled to disulfide oxidoreduction, the function of Mtb DsbE may be to ensure that secreted proteins are in their correctly folded states. We have determined the crystal structure of Mtb DsbE to 1.1 A resolution, which reveals a thioredoxin-like domain with a typical CXXC active site. These cysteines are in their reduced state. Biochemical characterization of Mtb DsbE reveals that this disulfide oxidoreductase is an oxidant, unlike Gram-negative bacteria DsbE proteins, which have been shown to be weak reductants. In addition, the pK(a) value of the active site, solvent-exposed cysteine is approximately 2 pH units lower than that of Gram-negative DsbE homologs. Finally, the reduced form of Mtb DsbE is more stable than the oxidized form, and Mtb DsbE is able to oxidatively fold hirudin. Structural and biochemical analysis implies that Mtb DsbE functions differently from Gram-negative DsbE homologs, and we discuss its possible functional role in the bacterium.

Amino Acid Sequence↗
PubMed2002

Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6.

In order to clarify their physiological functions, we have undertaken a characterization of the three-membered gene families SNZ1-3 and SNO1-3. In media lacking vitamin B(6), SNZ1 and SNO1 were both required for growth in certain conditions, but neither SNZ2, SNZ3, SNO2 nor SNO3 were required. Copies 2 and 3 of the gene products have, in spite of their extremely close sequence similarity, slightly different functions in the cell. We have also found that copies 2 and 3 are activated by the lack of thiamine and that the Snz proteins physically interact with the thiamine biosynthesis Thi5 protein family. Whereas copy 1 is required for conditions in which B(6) is essential for growth, copies 2 and 3 seem more related with B(1) biosynthesis during the exponential phase.

Blotting, Northern↗
PubMedDate not supplied

Functional analysis of shoulder arthrodesis.

The goal of this study was to determine the optimal position of shoulder arthrodesis for functional outcome and pain. Twenty patients who had undergone shoulder arthrodesis were interviewed and examined clinically and with standard radiographs. In addition, computed tomography (CT) scans were used to determine the exact position of the humerus relative to the scapula in all three planes. The average position observed was 14 degrees of flexion (humerus to longitudinal body axis), 55 degrees of abduction (humerus to lateral scapular border), and 23 degrees of internal rotation (forearm to sagittal body plane). Clinical evaluation showed functional advantages for tasks above waist level with increasing flexion but at the cost of more pain. Increasing abduction improved upper limb function above waist level but compromised complex movements below waist level. Higher degrees of abduction tended to improve the result expressed by the overall score and furnished better pain relief. Higher degrees of internal rotation resulted in improved function below waist level but also in more pain. Our results show that there is no single optimal position but suggest that a clinically estimated position of 15 degrees to 30 degrees of flexion, 35 degrees to 45 degrees of abduction, and 30 degrees to 40 degrees of internal rotation is desirable. This corresponds to CT-measured angles of 15 degrees to 30 degrees for flexion, 55 degrees to 65 degrees for abduction, and 0 degrees of internal rotation (humeral epicondylar axis to scapular plane).

Adult↗
PubMed2006

Expression and functional analysis of beta-adrenoceptor subtypes in rabbit submandibular gland.

beta-Adrenoceptors (beta-ARs) mediate important physiological functions in salivary glands. Here we investigated the expression and function of beta-AR subtypes in rabbit submandibular gland (SMG). Both beta(1)- and beta(2)-ARs, but not beta(3)-AR, were strongly expressed in rabbit SMG. beta(1)-AR proteins were widely expressed in acinar and ductal cells whereas beta(2)-AR proteins were mainly detected in ductal cells. A [(3)H]-dihydroalprenolol binding assay revealed that beta-AR B(max) was 186+/-11.9 fmol/mg protein and K(d) was 2.71+/-0.23 nM. A competitive binding assay with CGP 20712A, a beta(1)-AR antagonist, indicated that the proportion of beta(1)-AR and beta(2)-AR was 71.9% and 28.1%, respectively. Gland perfusion with the beta-AR agonist isoproterenol induced a significant increase in saliva secretion which was abolished by pretreatment with the non-selective beta-AR antagonist propranolol. Pretreatment with beta(1)- or beta(2)-AR selective antagonists, CGP 20712A or ICI 118551, diminished isoproterenol-induced increase in saliva secretion by 71.2% and 28.8%, respectively. The expression of alpha-amylase mRNA was significantly stimulated by isoproterenol, which was eliminated by propranolol and CGP 20712A. Perfusion with isoproterenol decreased alpha-amylase protein storage in SMG and increased alpha-amylase activity in saliva. These alterations became less significant after pretreatment with propranolol and CGP 20712A. Our results suggest that both beta(1)- and beta(2)-ARs are expressed in rabbit SMG. beta(1)-AR is the predominant subtype and may play an important role in regulating saliva and alpha-amylase secretion.

Animals↗
PubMed2004

Structure and functional analysis of the fungal galectin CGL2.

Recognition of and discrimination between potential glyco-substrates is central to the function of galectins. Here we dissect the fundamental parameters responsible for such selectivity by the fungal representative, CGL2. The 2.1 A crystal structure of CGL2 and five substrate complexes reveal that this prototype galectin achieves increased substrate specificity by accommodating substituted oligosaccharides of the mammalian blood group A/B type in an extended binding cleft. Kinetic studies on wild-type and mutant CGL2 proteins demonstrate that the tetrameric organization is essential for functionality. The geometric constraints due to the orthogonal orientation of the four binding sites have important consequences on substrate binding and selectivity.

Binding Sites↗
PubMed2000

Systematic function analysis of Bacillus subtilis genes.

Information on the complete genome sequence needs to be transformed into information related to function. Toward this goal, research consortia in Japan and Europe have been organized so as to acquire a collection of knockout mutants of genes with no established function. The current status of the Japanese project concerning mutant creation and characterization is summarized.

Bacillus subtilis↗
PubMed2000

A yeast-based genetic system for functional analysis of viral mRNA capping enzymes.

Virus-encoded mRNA capping enzymes are attractive targets for antiviral therapy, but functional studies have been limited by the lack of genetically tractable in vivo systems that focus exclusively on the RNA-processing activities of the viral proteins. Here we have developed such a system by engineering a viral capping enzyme-vaccinia virus D1(1-545)p, an RNA triphosphatase and RNA guanylyltransferase-to function in the budding yeast Saccharomyces cerevisiae in lieu of the endogenous fungal triphosphatase (Cet1p) and guanylyltransferase (Ceg1p). This was accomplished by fusion of D1(1-545)p to the C-terminal guanylyltransferase domain of mammalian capping enzyme, Mce1(211-597)p, which serves as a vehicle to target the viral capping enzyme to the RNA polymerase II elongation complex. An inactivating mutation (K294A) of the mammalian guanylyltransferase active site in the fusion protein had no impact on genetic complementation of cet1Deltaceg1Delta cells, thus proving that (i) the viral guanylyltransferase was active in vivo and (ii) the mammalian domain can serve purely as a chaperone to direct other proteins to the transcription complex. Alanine scanning had identified five amino acids of vaccinia virus capping enzyme-Glu37, Glu39, Arg77, Glu192, and Glu194-that are essential for gamma phosphate cleavage in vitro. Here we show that the introduction of mutation E37A, R77A, or E192A into the fusion protein abrogates RNA triphosphatase function in vivo. The essential residues are located within three motifs that define a family of viral and fungal metal-dependent phosphohydrolases with a distinctive capacity to hydrolyze nucleoside triphosphates to nucleoside diphosphates in the presence of manganese or cobalt. The acidic residues Glu37, Glu39, and Glu192 likely comprise the metal-binding site of vaccinia virus triphosphatase, insofar as their replacement by glutamine abolishes the RNA triphosphatase and ATPase activities.

Acid Anhydride Hydrolases↗
PubMed2005

Functional analysis of the chicken delta1-crystallin enhancer activity in Drosophila reveals remarkable evolutionary conservation between chicken and fly.

Functional conservation of enhancers among evolutionarily diverged organisms is a powerful way to identify basic regulatory circuits and key developmental regulators. This is especially applicable to Crystallin genes. Despite unexpected heterogeneity and diversity in their DNA sequences, many studies have revealed that most of the Crystallin genes are regulated by a relatively small set of developmentally important transcription factors. The chicken delta1-crystallin is one of the best-characterized Crystallin genes. Its lens-specific regulation is governed by a 30 bp long DC5 fragment present in the third intron of the gene. DC5 contains PAX6 and SOX2 binding sites, and its activity depends on the cooperative binding of these two transcription factors. To test the idea that Pax6 and Sox2, together with the DC5 enhancer, could form a basic regulatory circuit functional in distantly related animals, we introduced the DC5 fragment into Drosophila and studied its activation pattern and regulation. The results show that the DC5 enhancer is not only active in the compound eye but, remarkably, is specifically active in those cells responsible for Crystallin secretion in Drosophila, i.e. the cone cells. However, regulation of the DC5 enhancer is carried out not by Pax6, but by Pax2 (D-Pax2; shaven--FlyBase) in combination with the Sox2 homologue SoxN. Both proteins (D-PAX2 and SOXN) bind cooperatively to the DC5 fragment and activate the enhancer synergistically. As PAX6 and PAX2 proteins derive from the same ancestor, we propose that during evolution Pax6 function in vertebrate lens development was retained by Pax2 in Drosophila.

Animals↗
PubMed2004

An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation.

FOXL2 is a forkhead transcription factor involved in ovarian development and function. Here, we have studied the evolution and pattern of expression of the FOXL2 gene and its paralogs in fish. We found well conserved FoxL2 sequences (FoxL2a) and divergent genes, whose forkhead domains belonged to the class L2 and were shown to be paralogs of the FoxL2a sequences (named FoxL2b). In the rainbow trout, FoxL2a and FoxL2b were specifically expressed in the ovary, but displayed different temporal patterns of expression. FoxL2a expression correlated with the level of aromatase, the key enzyme in estrogen production, and an estrogen treatment used to feminize genetically male individuals elicited the up-regulation of both paralogs. Conversely, androgens or an aromatase inhibitor down-regulated FoxL2a and FoxL2b in females. We speculate that there is a direct link between estrogens and FoxL2 expression in fish, at least during the period where the identity of the gonad is sensitive to hormonal treatments.

Animals↗